These exercises are about manipulate single-cell data with Seurat. Please download the counting matrix from BOX and loading them into a Seurat object. Or you may also used the rds file data/scSeq_CKO_sceSub.rds.
Exercise 2 - Data manipulation with Bioconductor packages
## Warning in xy.coords(x, y, xlabel, ylabel, log): 1 y value <= 0 omitted from
## logarithmic plot
## DataFrame with 400000 rows and 5 columns
## Total LogProb PValue Limited FDR
## <integer> <numeric> <numeric> <logical> <numeric>
## CCACGGAAGCTCTCGG-1 0 NA NA NA NA
## TGTGGTAAGAGTCGGT-1 2 -11.1237 0.7561244 FALSE 0.99174
## CCCTCCTTCGTCTGCT-1 2 -18.2572 0.0727927 FALSE 0.66022
## ACTGAGTGTGTCGCTG-1 0 NA NA NA NA
## CGTAGCGTCTCTGCTG-1 0 NA NA NA NA
## ... ... ... ... ... ...
## AGAGCTTGTCCGACGT-1 0 NA NA NA NA
## GCTGCGACAATAGCAA-1 0 NA NA NA NA
## CGAACATAGTGAAGTT-1 2 -12.3017 0.632437 FALSE 0.99174
## TAGCCGGCATGTCGAT-1 0 NA NA NA NA
## CGAGAAGAGCAGATCG-1 0 NA NA NA NA
## Mode FALSE TRUE NA's
## logical 211696 2110 186194
## Limited
## Sig FALSE TRUE
## FALSE 209919 1777
## TRUE 1 2109
## ENSMUSG00000051951 ENSMUSG00000025902 ENSMUSG00000033845 ENSMUSG00000025903
## 1.669575e-07 1.669575e-07 1.407972e-04 5.201547e-05
## ENSMUSG00000104217 ENSMUSG00000033813
## 1.669575e-07 6.783772e-05
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.0422 0.3840 0.7385 0.9630 1.3082 7.2457
##
## no yes
## 2004 106
## Warning: Removed 2785 rows containing non-finite values (stat_density).